[English] 日本語
Yorodumi
- EMDB-3577: MTA2-RBBP7 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3577
TitleMTA2-RBBP7 complex
Map data
Sample
  • Complex: MTA2-RBBP7 complex
    • Other: MTA2-RBBP7 complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 38.0 Å
AuthorsBrasen C / Dorosz J / Wiuf A / Boesen T / Mirza O / Gajhede M
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2017
Title: Expression, purification and characterization of the human MTA2-RBBP7 complex.
Authors: Christoffer Brasen / Jerzy Dorosz / Anders Wiuf / Thomas Boesen / Osman Mirza / Michael Gajhede /
Abstract: The repressive Nucleosome Remodeling and histone Deacetylation (NuRD) complex remodels the chromatin structure by coupling ATP-dependent remodeling activity with histone deacetylase function and ...The repressive Nucleosome Remodeling and histone Deacetylation (NuRD) complex remodels the chromatin structure by coupling ATP-dependent remodeling activity with histone deacetylase function and plays important roles in regulating gene transcription, DNA damage repair and chromatin assembly. The complex is composed of six subunits: Metastasis Associated proteins MTA1/2/3 initially recruit histone chaperones RBBP4/7 followed by the histone deacetylases HDAC1/2 forming a core complex. Further association of the CpG-binding protein MBD2/3, p66α/β and the ATP-dependent helicase CDH3/4 constitutes the NuRD complex. Recent structural studies on truncated human proteins or orthologous have revealed that the stoichiometry of the MTA1-RBBP4 complex is 2:4. This study reports expression and purification of the intact human MTA2-RBBP7 complex using HEK293F cells as expression system. In analogy with findings on the Drosophila NuRD complex, we find that also the human MTA-RBBP can be isolated in vitro. Taken together with previous findings this suggests, that MTA-RBBP is a stable complex, with a central role in the initial assembly of the human NuRD complex. Refined 3D volumes of the complex generated from negative stain electron microscopy (EM) data reveals an elongated architecture that is capable of hinge like motion around the center of the particle.
History
DepositionJan 17, 2017-
Header (metadata) releaseFeb 15, 2017-
Map releaseMay 3, 2017-
UpdateMay 3, 2017-
Current statusMay 3, 2017Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3577.png

Downloads & links

-
Map

FileDownload / File: emd_3577.map.gz / Format: CCP4 / Size: 18.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.15 Å/pix.
x 170 pix.
= 535.5 Å		3.15 Å/pix.
x 170 pix.
= 535.5 Å		3.15 Å/pix.
x 170 pix.
= 535.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.005 / Movie #1: 0.02
Minimum - Maximum-0.032571185 - 0.10222287
Average (Standard dev.)0.00017141107 (±0.0044833473)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions170170170
Spacing170170170
CellA=B=C: 535.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.153.153.15
M x/y/z170170170
origin x/y/z0.0000.0000.000
length x/y/z535.500535.500535.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS170170170
D min/max/mean-0.0330.1020.000

-
Supplemental data

-
Sample components

-
Entire : MTA2-RBBP7 complex

EntireName: MTA2-RBBP7 complex
Components
  • Complex: MTA2-RBBP7 complex
    • Other: MTA2-RBBP7 complex

-
Supramolecule #1: MTA2-RBBP7 complex

SupramoleculeName: MTA2-RBBP7 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F / Recombinant plasmid: pOPINHALO7/pOPINF

-
Macromolecule #1: MTA2-RBBP7 complex

MacromoleculeName: MTA2-RBBP7 complex / type: other / ID: 1 / Classification: other
Source (natural)Organism: Homo sapiens (human)
SequenceString: MAANMYRVGD YVYFENSSSN PYLVRRIEEL NKTANGNVEA KVVCLFRRRD ISSSLNSLAD SNAREFEEE SKQPGVSEQQ RHQLKHRELF LSRQFESLPA THIRGKCSVT LLNETDILSQ Y LEKEDCFF YSLVFDPVQK TLLADQGEIR VGCKYQAEIP DRLVEGESDN ...String:
MAANMYRVGD YVYFENSSSN PYLVRRIEEL NKTANGNVEA KVVCLFRRRD ISSSLNSLAD SNAREFEEE SKQPGVSEQQ RHQLKHRELF LSRQFESLPA THIRGKCSVT LLNETDILSQ Y LEKEDCFF YSLVFDPVQK TLLADQGEIR VGCKYQAEIP DRLVEGESDN RNQQKMEMKV WD PDNPLTD RQIDQFLVVA RAVGTFARAL DCSSSIRQPS LHMSAAAASR DITLFHAMDT LQR NGYDLA KAMSTLVPQG GPVLCRDEME EWSASEAMLF EEALEKYGKD FNDIRQDFLP WKSL ASIVQ FYYMWKTTDR YIQQKRLKAA EADSKLKQVY IPTYTKPNPN QIISVGSKPG MNGAG FQKG LTCESCHTTQ SAQWYAWGPP NMQCRLCASC WIYWKKYGGL KTPTQLEGAT RGTTEP HSR GHLSRPEAQS LSPYTTSANR AKLLAKNRQT FLLQTTKLTR LARRMCRDLL QPRRAAR RP YAPINANAIK AECSIRLPKA AKTPLKIHPL VRLPLATIVK DLVAQAPLKP KTPRGTKT P INRNQLSQNR GLGGIMVKRA YETMAGAGVP FSANGRPLAS GIRSSSQPAA KRQKLNPAD APNPVVFVAT KDTRALRKAL THLEMRRAAR RPNLPLKVKP TLIAVRPPVP LPAPSHPAST NEPIVLED MASKEMFEDT VEERVINEEY KIWKKNTPFL YDLVMTHALQ WPSLTVQWLP EVTKPEGKDY ALHWLVLGT HTSDEQNHLV VARVHIPNDD AQFDASHCDS DKGEFGGFGS VTGKIECEIK I NHEGEVNR ARYMPQNPHI IATKTPSSDV LVFDYTKHPA KPDPSGECNP DLRLRGHQKE GY GLSWNSN LSGHLLSASD DHTVCLWDIN AGPKEGKIVD AKAIFTGHSA VVEDVAWHLL HES LFGSVA DDQKLMIWDT RSNTTSKPSH LVDAHTAEVN CLSFNPYSEF ILATGSADKT VALW DLRNL KLKLHTFESH KDEIFQVHWS PHNETILASS GTDRRLNVWD LSKIGEEQSA EDAED GPPE LLFIHGGHTA KISDFSWNPN EPWVICSVSE DNIMQIWQMA ENIYNDEESD VTTSEL EGQ GS
Recombinant expressionOrganism: Homo sapiens (human)

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
StainingType: NEGATIVE / Material: uranyl formate

-
Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 10.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 38.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1267
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more